How old are the ducks? If they are same age as the chickens they could be going through their "teen-age" phase. During this time they can and often are especially nervous and flighty.
Try to spend as much time in there with them as you can. I suggest sitting down and talking very calmly to them, while offering yummy treats. I gave mine lots of fresh veggies by hand, would toss them slugs I picked from the garden, and even meal worms. Needless to say, I became the goddess of food, and seen in a much happier light. They still can be quite flighty at times, but so long as I move slowly, talk softly and calmly, they will let me approach and sometimes pick them up with little hassle. If I sit or squat down they will approach me, and frequently follow me around as I work around in their yard (mostly because I think they are gobbling up whatever bigs I stir up in the process).
Sorry to hear about your loss, but be patient and in time they should turn around a be ok.
